Star Wars: the Shadow Order
by Mirouku
Summary: Follow the story of an ARC Trooper who has to choose between being a good soldier and follow Order 66 or turning his back on his brothers to save the general Jedi Master Shaak Ti. What will be the consequences of his actions, and will he be able to live with himself? This is set in a alternate universe mixed between Cannon, Legends, and my own preferences.
1. Call Over Felucia

Preface: I wanted to give you a little background of the story you are about to read and the person who is currently writing it. I am twenty-five and I am a big fan of Star Wars I am both a fan of the Canon we now have and of the EU. I have taken things from both sides of the coin and writing my own story. I am a huge fan of the Clone Wars and I don't believe enough attention has been pushed to see things through their eyes. So not only will this mostly be through the eyes of a clone but also bring back some Jedi who fell in the purge and those that lived. Of course I would appreciate any and all help and reviews, but do keep in mind its been three years since I have attempted writing.

Some of you may think you have heard all there is to know about what took place. Honestly sometimes it is hard to determine the truth from fiction, a reality from a dream. I am unsure why I feel the need to share my story, but I want it to be known what occurred what seems so long ago.

I have not been involved with the amount of conflicts as my brothers have nor am I as old as they are in theoretical terms. I was one of the last to come from Tipoca City that actually saw combat before the Order. I was what most consider a teenager at the Battle of Kamino. I got to train under the supervision of Commander Colt. While I wasn't tops in either physical strength or overall prowess within my squad. I am an ARC. An ARC trooper could match any weakness to a normal troopers greatest strength and hold his own. Where I excelled, overwatch and close quarters combat, few in the company could match my skills. I guess I am getting a little ahead of myself. I am CT-3740 also known as Brute I am or was in Echo Squad. Toward the end of the Clone Wars my squad was selected to provide emergency reinforcements to Felucia. General Shaak Ti herself was ordered away from Kamino after some debacle on Coruscant she was involved in. The rumors coming through the ranks about Fives and his message about the entire Clone Wars made every man involved question everything about the war. Rancor Battalion was selected to also go to Felucia to reinforce the 327th Star Corps led by General Aayla Secura. The reason for such heavy reinforcements was that the Separatist had dug into the planet, but was on the verge of losing its hold there so the orders came down to make sure we took it at all cost. General Barriss Offee was already there as well as a few other commanders and generals alike. The mission had started normal; disembarked from Venator-class Star Destroyer "The Intrepid" on our Larty. I happened to be in the same one with General Shaak Ti with the rest of Echo Squad with some Galactic Marines in tow, and another ARC squad. Normally we would carry thirty among us, but with the escort of the ARC-170s flying as guards, there were roughly twenty men; two ARC squads the General and the marines. Shaak Ti thought it wise to have fewer troops, and equipment for mobility.

When it happened in truth I was hoping to come across an Acklay to see if I had enough precision to take one in a single shot, but the room went gravely quiet as everyone's HUDs flashed on unexpectedly. The comms set to private within our helmets connected troopers only; blocking the outside world and our HUDs lit up to Commander Bly's vision the order came. Growing up we were instilled to memorize all of these safety protocols to protect the Republic from falling. Order 66 happened to name all Jedi as enemies of the Republic, and to kill without prejudice. When this order came through you were among three categories; you either attacked your general, you hesitated and most likely died, or you killed your brothers for the life of the generals. Watching the horizon light up in blue blaster fire as you approached your drop zone was one of the most terrifying visions to witness; having front row seats to seeing Commander Bly turn on his men fighting to the death was another sensation altogether. I didn't hesitate, and I don't know why, but my vibroblade went straight through the throat of the brother raising his weapon next to me. Everything seemed to go into slow motion without hesitation I moved on to more men. Watching Bly fall to the ground assuming the worst as his HUD blinked out, the Larty shook as two of the ARC-170s fell from the sky, my only hope was for the one who shot them down was with me on this fight, but I had to live to find out. The inside of the Larty was chaos brother shot and stabbed at another, men who grew up in the same squad together killing their closest friends. Pain flaring through me as my wounds became prevalent as a fellow ARC fell to my vibroblade. My eyes locking on my fellow squad mate, raising his blasters towards me told me what side he chose. No hesitation my body threw itself into my natural instincts as I quickly closed the gap on…my enemy. What seemed like a lifetime probably lasted less than thirty seconds, but by the end I collapsed. I knew I was going to die I didn't know which wound had done the job, was it the DC blaster wound to the chest from a fellow ARC or the vibroblade to the stomach, I wasn't sure all I know is two of my brothers from my squad was felled by my hands because I decided to defend the general. The last thing I was going to see is my squad mate with my vibroblade buried in his chest with the smoking DC-15A in his hand from shooting me, in that moment I wanted to live so I would know I made the right choice, but I also wanted to accept the sweet embrace of the end so I could never be haunted by this day.

Where was I, what happened… the calling of a wounded brother stirred me. I woke in a cold sweat trying to move quicker than my body could follow, and the adrenaline induced strength evaporated before I could even raise up, and I fell back onto my makeshift bed. Withering in pain as the hot humid air filled my lungs, rasping for breath looking back into a mirror. The voice coming from the image before me wasn't my own it was similar, but not mine it told me to relax, and I was luckily going to live; things went black after I heard him. When I next woke it was dark out and the calls of the jungle woke me, the same man was there.

"Where am I? What happened?" I weakly asked, staring at him hoping for the full explanation of today's events.

"First I am CT-9635, also known as Doc, from the 327th, " he explained calmly, "The where is rather simple, we are on Felucia currently in a field hospital till Evac or death greets us."

"Why would death, you didn't answer my second question Doc," I told him coldly, anger slowly stirring at his words.

Doc explained that Order 66 was issued by the Supreme Chancellor Sheev Palpatine stating that the Jedi had attempted to overthrow the Chancellor and take the Republic for their control. Currently the bridge and communications had been taken over on The Intrepid, but the ship was still being fought over between Clones who had sided with the Jedi and those loyal to the Republic if there was a difference. He also explained that several Padawans had survived on Felucia where their Masters had not, and that only General Aayla Secura, and General Shaak Ti were the only known generals to have survived on Felucia. Apparently my Larty was a warzone as only the general actually walked out once it landed. Only three had lived from it, a fellow Echo Squad, and a Marine both wounded and less likely to live than myself. The 327th stood intact and mostly sided with the Jedi, but Bly and several of his men fell defending the Aayla Secura , and Barriss Offee in the beginning. General Offee was among the dead accounted for on Felucia. I passed out shortly after being told that the Intrepid would either be our savior or our death.

I awoke to the sound of a medical droid entering the room. The unmistaken sound of the droids shuffling announced it as a 2-1B surgical droid the hydraulic movement of gears wasn't very quiet in the small room.

"What time is it, and where are we?" I asked through gritted teeth as I struggled to rise up in the bed. The burning of still mending muscles reminding me of the wounds I had recently suffered.

"Greetings CT-3740, I will be checking your vitals," the animatronic voice announced.

"They call me Brute, now what time is it and where are we?" I asked again, annoyance quickly building with this droid as the sound of whirring began.

"Patient name changed to Brute, clone name CT-3740 preference Brute. Greetings Brute I will be checking your vitals," the voice repeated. The whirring noise again coming from the droid as it began reading the monitors.

"Alright, what time is it and where are we?" The clone asked the burning slowly fading and the pain subsiding.

The droid began spouting off its findings and medical analysis as if the clone wasn't there.

"Patient CT-3740 also known as Brute is recovering slowly, low bacta supplies forces mundane treatment. Pain management for check administered. Blood pressure is up as well as signs of stre-"

"Hey droid I told you its Brute, just Brute!" The clone growled.

The whirring began as the droid processed the newest information.

"Patient just Brute, is experiencing continued elevation of blood pressure. Consider administering medication to treat newest ailment and access potential cause."

The exacerbated clone fell back into his bed, and closed his eyes waiting for the droid to finish and leave the room.

"If only I had some tools I would dismantle this rust bucket," grumbling quietly to himself.

The fading sounds of the hydraulics announcing the droid heading for the door. The quiet gears timidly cranking as the droid turned at the door.

"Just Brute, it is 0900, and we are on The Intrepid, you have been in my care for the last two weeks. The current commander of this vessel is General Shaak Ti" the droid announcing in a bit of the sarcastic tone before walking away silently.

The clone left lying there staring at the door where the droid had been. Four figures entered as the droid left. First was General Shaak Ti the red skin of a Togruta was easy enough to spot, a blue Twi'Lek that could only be General Secura, the third was another red skinned individual that wasn't recognizable off hand but a lightsaber was clipped to the belt, behind her was a clone the armor a dark green that was beyond battle marred, the kama announced him as a commander. The three who didn't have their face covered seemed to be a mixture of emotion it was evident throughout the figures the outcome of Order 66 did not seem to go as well as it had on Felucia.

"Looks like the droid won't be forgiving you so easily since you attempted to stab it when we moved you to the ship. Thank you for assisting me on the LAAT," a soft serene voice from Shaak Ti interrupted the silence, "I regret to inform you the other two survivors were not as lucky as you were."

The feeling that sunk into the pit of my stomach as I realized I was the only Echo left, "So rumor that came from Fives was real general?" My voice didn't even sound like my own.

"Yes, he was telling the truth, and I am glad Commander Fox was able to capture him without anyone knowing he lived." The general's words barely registered before my will took over and I rose out of bed. The healed wounds in my abdomen and chest screamed from being freshly mended.

"Fives is alive," my voice no longer under control as my surprise was clear raising my voice, "How did he live the whole Rancor Battalion heard the rumors of him being killed on Coruscant!"

The red skinned individual spoke up and explained her name was Tiplee, she was Mikkian, and that her sister General Tiplar had died due to a premature call of the order within her ranks. The premature call of the order caused Palpatine to try to cover it up and Fives had discovered the truth and spread it as quickly as possible. The word hadn't got out as quickly as the Jedi involved had hoped before Fox had to bring Fives in for his safety. The order was issued shortly after, and that sides had been drawn with Felucia coming out better than most war fronts had apparently. The Intrepid had fallen in the hands of the Jedi's clones and we were in orbit in the Outer Rim hoping to hear from anyone. General Kenobi has just issued an order that the Jedi Order on Coruscant had fallen and that the temple was no longer safe for Jedi. The hologram did allow for a hidden message to be administered to the highest members of the Order and luckily the enemy had not learned of the coded signal in the hologram yet. A list of hidden locations had been given to members in case the temple ever fell there would be a safe place to retreat. The location had not been disclosed yet, but we were assured Shaak Ti would reveal it in time.

Tiplee had just finished explaining everything when she introduced Commander Doom, of the 27th Legion. He waited till the Jedi walked out when Doom stepped up to the bed and spoke.

"I am surprised an ARC would turn on his brothers," the distaste seemed evident, "but I understand why you did it. I know it wasn't easy for you to make that decision, it wasn't for me."

My silence seemed be the green flag for him to continue speaking. The numbers hadn't come in yet nor had any further orders or communication. There wasn't any telling exactly how many men we had on our side or even how many Jedi survived. The only thing for sure was most of the Coruscant Guards would be joining us, and a good amount of ARCs had decided to listen to Fives. I would most likely be looking at a promotion to help fill in the need for officers. The hardest pill to swallow was twofold the first being that Republic loyal clones had hit the field hospital making their last stand for the Republic on Felucia and that was how my two comrades had perished, and Doc had been killed as well. The second was the very Republic so much was sacrificed for was no more. After Order 66 the Supreme Chancellor called an emergency session in the Senate deeming all Jedi as traitors of the Republic. The Republic had now become the Empire.

After speaking with Commander Doom I didn't have much to say when the rumors of what had occurred on Coruscant and Fives everything had come into question, the ripple had caused many clones to contemplate where this was going, how much could possibly mean how much of it was true, and what was our life going to be after war. None of this had been answered because now the only thing I knew for sure was even though the Clone Wars had ended the Republic; the war had truly just begun.


	2. Coruscant Rescue

In orbit over Felucia, on board "The Intrepid", three weeks after Order 66.

The echo of boots tapping along the darkened deserted hall, as a lone clone limped slowly to the Command Bridge all non-essential personnel ordered to the lower areas of the ship. The still mending wounds causing the trooper to double over in pain as an especially rough stab shook his body. The weight of the newly polished armor irritating the wounds to Brute's stomach made it almost impossible to keep walking, but the ARC forced himself on. Groaning loudly as the mechanical stomping was heard approaching behind him.

"Just Brute, you are in no condition to be this far from the Medical Bay, and as your caretaker I advise you to come with me at once," the 2-1B Medical droid announced firmly down the hall.

"Rust bucket you come near me, and I will stab you this time. There is a meeting on the Command Bridge and I am needed there." Brute gritted through his teeth as he forced himself to keep going down the hall.

The extra weight of the pauldrons and kama on his newly polished uniform added more weight than the recovering body could really hold. Chest piece stained blue with a red hand pressed firmly on the left breast announced a new company for him, Commander Doom thought appropriate for him to Captain.

The 2-1B droid finally catching up to Brute, grabbed onto the back of his Kama and help guide him and holds him up to finish the last leg down the dark hall. The emergency flashing lights the only thing illuminating the dark hall.

"Sir, you really should listen to your medical professional, about your care," the droid quietly told the struggling clone as the door to the Command Bridge slowly opened permitting them entrance.

Brute glanced across the room to take into account that all was there, he had heard rumors of other units, commanders, and Jed making it to them but no official names or numbers had reached him in the Medical Bay. His eyes immediately spotted the three Jedi who visited him, as well as Commander Doom. Beside Shaak Ti stood a Kel Dor, and a young Togruta he had never seen before. The few clones present he recognized beyond Doom, he recognized Captains Jag and Stone. His eyes lit in surprise as he took in the two clones that were across the Kel Dor and Togruta, he was shocked they would side against the Republic it was Rex, and Wolfe the holovid obscuring them, but their armor markings made them known, which identified the two Jedi immediately as Ahsoka Tano, and Plo Koon. His thoughts trailing at how these two Jedi could possibly escape the massacre that occure-

"Captain Brute I was unaware that Medical had cleared you yet, care to join us or do you want Lieutenant Corric to deal with your mission assignment? Captain Doom's voice boomed in the Command Room jarring him from his thoughts, the Captains eyeing the medical droid holding Brute up.

"Yes Sir." The sharp quick snap of a response bringing back memories of Kamino, shrugging off the help of the droid as I began to take brisk calculated steps so I could reach the holotable without displaying the weakness too obviously.

Listening to Rex explain the circumstances that we were in, now that we had deserted the Republic now the Empire, the situation was grave indeed. We had allies within the senate, but not where they could publically help. It would all be slow and quiet. The two locations General Kenobi had selected as a new starting point were smart. One planet selected by the General he had never come across on a map. As it stood we were floating in the dark vast space in the galaxy while we waited for clearance on the two locations. As a whole we were vastly outnumbered, gunned, and supplied. Final tallies on Jedi were grim. Nearly ten thousand Jedi was down to less than two hundred, and even then that was a guaranteed higher number than reality. With roughly forty five thousand men currently crammed into all the vessels we held, and a small fleet our life support system was running over time to keep oxygen levels up. Fuel was being spent at a higher pace which is why only necessities were being run, and normally two year supply of food has now turned to less than six months. Another five thousand men of the Coruscant Guard waited on Coruscant for pick up under Captain Fox and Arc Trooper Fives, and that's where Brute comes in.

"Captain Brute, there is a transport vessel sent by Alderaan. They are there to get supplies and ship them out to the Outer Rim. They were given a contract months ago to ferry supplies to restock major war fronts. Intel says this is the last shipment until reorganization and new contracts are up for bids. The supplies will give us enough fuel, and food to last us an extra six months on full burn. There is also enough space to bring the last of the men with what Jedi's they recovered. There is at least three Jedi currently with Fox and Fives. You will have to take the ship by force, and you have to hold the position long enough to get everyone on, and remove any tracking possible on the ship. If you or your men fail to do this we will not be able to rescue you or anyone there. There will not be a ship waiting for you. We are sending you and your men down in a Larty that will align with the patrols on Coruscant." Rex spoke in a grim tone spelling it out for everyone in the room.

The mission was to Coruscant the heart of the newest enemy's territory. We had thousands of men behind enemy lines risking their lives for what Jedi they could round up and safely keep from certain death. The only hope to bringing them out safely rested on Brute and his Company's ability to take the Coruscant docks by force and hold it long enough to bring the rest of our men out in the middle of space. What it boils down to this was a suicide mission, and he had to command the deaths of men he hadn't even had the chance to meet yet.

Doom spoke up, "Captain Brute, in your current Medical condition you were authorized and advised to remain on The Intrepid while your men went in. Lt Corric has been here taking down notes and studying Coruscant and its security protocols. Your company was selected for this mission, but you should remain."

"All due respect Sir, but I will have to go against the decision to remain with the ship. If my Company is going into battle, one that spells certain death I am at least going to be among them." Brute replied in grim solace as he resigned himself to his fate that awaited Coruscant .

Brute was sitting in his officer quarters, one of the few rooms left on the ship reserved for Jedi or Captains, him a Captain, but of what, there was no longer a GAR its mantra of living forever failed three years after its inception. With his DC-15s already in his ankle holster Brute was scouring over his two DC-17 blasters, when he heard someone wrapping on his door.

"Come in." Brute said announced.

Lt. Corric stepped in and stood at attention, his armor painted in the fashion of Brute's. His hand saluting what he viewed his commanding officers.

"At ease, and say what you need." Brute's response was quick and precise no time for annoying protocols.

"Sir, Lt Corric reporting in, we have orders to mobilize in six hours, and we will be flying out. General Shaak Ti has requested to personally go on this mission and on the Larty with you, Sir," Corric said without evening pausing.

"Dismissed Corric, get the men briefed, and ready to go. Those who survive I will meet after the mission."

Brute didn't see the point in meeting dead men, but he wasn't trained to be a Captain, he was trained as an ARC a living squad. Captains were of little consequence unless you were on a ship. In the field it was just you and your brothers.

Flying over Coruscant, on board M1 Larty command transport, 15 minutes till blackout.

General Shaak Ti meditated quietly in the corner of the transport, Brute checking his specs one last time till landing.

Brute waited till the piloted finished relaying the falsified flight charts for Coruscant Security. His instructions breaking the silence that threatened to send the troops to despair.

"Listen up, when boots hit duracrete its black out, no HUDs, no helmet specs, follow your squad's signals and watch your movements. Anything that shoots at you shoot back. This is a command I never expected to order. If you or a brother is under threat of being taken, shoot to kill this includes on the General and do not be taken, "Brute's voice took on a somber tone. "Our only hope of surviving the newest war we have found ourselves in is to make sure our command stays safe, hidden, and protected. We are the last of the GAR. "

Brute finished his speech and stood next to Shaak Ti. Looking down at the Togruta he saved back on Felucia, wondering why she volunteered for a mission that she didn't have to go on. With the descent occurring rapidly the voice from the cockpit announcing they are breaking flight plans and to change course, communications cut. Ten feet above duracrete the sound of fighters being launched and the Larty be sent on a wayward journey on auto with full burn. Less than ten seconds and the explosions of the other Lartys being hit all four squads had hit the ground moving. Blaster fire ripped through the streets as the men took the Spaceport. Humans and clones raised their weapons against the newest squad. Shaak Ti's blue saber was out as her force powers made her nearly a blur as she flashed through the guards in the port. Red and blue flares launched high in the Coruscant sky the ship had been taken. Weapons, armor, fuel, medical, food, everything we needed to survive was in our grasp now we had to hold. A wave of clones began pouring from the city three separate locations each guided by a bright lightsaber. Fire began raining down on the platform as ships converged on it. The Acclamators gun's returned fire; at least three turbolaser's lashed out against the assault of fighters taking parts of Coruscant with them, anti-aircraft turrets lit up the spaceport as strafing runs were made the fearless clones fighting their enemy and standing their ground. Troops filing into the Acclamator as more turbolasers turned online the less fire was being rained down upon us. Lt. Corric's squad being spotted at the entrance to the spaceport holding his ground and firing against the enemies attempts to retake the port. The orange flare firing high into the sky and erupting to be heard over the gun fire signaling time to launch. The loyal Corscuant Guard striking from all entry ways slowly overwhelming the squad standing its ground Brute watching as the few left on the platform attempted cover fire. Corric's squad being cut off from retreat more fire rained down upon their position trying to reopen the gap for the few left standing to escape; solders begin to march up the platform. Brute made the call for all to pull back to the ship. The trapped squad having their fate sealed in the entry way.

Corric heard the propulsion system beginning to fire, his squad trapped less than a third of them stood still as blaster bolt flew past them. Corric returned fire making it a worthy last stand having been pushed from his original position, his men tried covering the entry to the platform, but they were being hammered his only option to guarantee them enough time to launch safely was suicide. Taking his last thermal detonator out, he signaled his final command. Not to be taken alive was his only option hitting the center as the red began flashing in his hands, his men following suit as they charged behind cover becoming moving bombs. Most hit the ground as soon as they left cover. The blinding flash as multiple detonators began destroying the entry of the spaceport. The Accalamtor souring through Coruscant sky launching from the bay, turbolasers laying waste to the city.

In orbit above Felucia, Command Bridge on The Intrepid, 24 hours after Coruscant Rescue

Brute stood on the bridge besides the newly recovered Captain Fox and ARC Trooper Fives listening to both Rex and Doom for his debriefing. His mission was a complete success by their numbers. Less than two squads perished on Coruscant, and nearly five thousand clones recovered as well as five Jedi. Brute was eyeing the six that stood in the corner Shaak Ti debriefing the five others that stood before her.

The elderly human female Master Jocasta Nu fled with who she could after holding up in the Jedi Archives and recovering what Jedi Holocrons she could the valuable data she saved or destroyed was a key to saving the Order. The other was a much younger human female Master Fy-Tor-Ana an instructor from the temple who escaped with Nu and the two padawans with her. One the young brown skinned Zabrak her golden braids swinging from her head as her façade began to crumble as she learned the fate of the Order at the hands of the Empire. Padawan Drakka Judarrl was her name Brute was finding it hard to look at her crying. Moving on to the other who stood there evident anger emanating off her another female Zabrak Padawan Maris Brood and beside her the Jedi Knight Rune a Mon Calamari, both seemed be rocked in their turmoil as the truth must have hit them like a wave that the Order had all but been obliterated with a few short weeks. In the end we had ships, supplies, and now the location of where we were rebuilding. This war is not over yet. 


End file.
